Declare the primary genome in pipeline jobs rather than infer it

SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/AlignmentImportInitTask.java

@@ -132,7 +132,7 @@ private List<AnalysisModel> parseAndCreateReadsets() throws PipelineJobException
                         }
                     }
 
-                    getPipelineJob().getSequenceSupport().cacheGenome(SequenceAnalysisService.get().getReferenceGenome(o.getInt("library_id"), getJob().getUser()));
+                    getPipelineJob().getSequenceSupport().cacheGenome(SequenceAnalysisService.get().getReferenceGenome(o.getInt("library_id"), getJob().getUser()), true);
                     getPipelineJob().getSequenceSupport().cacheReadset(r);
                 }
             }

SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/AlignmentInitTask.java

@@ -156,7 +156,7 @@ else if (steps.size() > 1)
                     throw new PipelineJobException("Reference file does not exist: " + refFasta.getPath());
                 }
 
-                getPipelineJob().getSequenceSupport().cacheGenome(output.getReferenceGenome());
+                getPipelineJob().getSequenceSupport().cacheGenome(output.getReferenceGenome(), true);
 
                 getHelper().getFileManager().addStepOutputs(action, output);
                 getHelper().getFileManager().cleanup(Collections.singleton(action));

SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceAlignmentJob.java

@@ -29,6 +29,8 @@
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
+import java.util.Set;
+import java.util.stream.Collectors;
 
 /**
  * User: bimber
@@ -125,7 +127,28 @@ public SequenceReadsetImpl getReadset()
 
     public ReferenceGenome getTargetGenome()
     {
-        return getSequenceSupport().getCachedGenomes().isEmpty() ? null : getSequenceSupport().getCachedGenomes().iterator().next();
+        if (getSequenceSupport().getCachedGenomes().isEmpty())
+        {
+            return null;
+        }
+        else if (getSequenceSupport().getCachedGenomes().size() == 1)
+        {
+            return getSequenceSupport().getCachedGenomes().iterator().next();
+        }
+
+        // Cannot infer the correct genome. We assume it was set upstream:
+        if (getSequenceSupport().getPrimaryGenomeForJob() == null)
+        {
+            throw new IllegalStateException("The primary genome ID has not been set");
+        }
+
+        Set<ReferenceGenome> passing = getSequenceSupport().getCachedGenomes().stream().filter(x -> getSequenceSupport().getPrimaryGenomeForJob().equals(x.getGenomeId())).collect(Collectors.toSet());
+        if (passing.isEmpty())
+        {
+            throw new IllegalStateException("No cached genome with ID: " + getSequenceSupport().getPrimaryGenomeForJob());
+        }
+
+        return passing.iterator().next();
     }
 
     public static final String NAME = "sequenceAnalysisPipeline";

SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceJobSupportImpl.java

@@ -3,6 +3,7 @@
 import com.fasterxml.jackson.databind.JavaType;
 import com.fasterxml.jackson.databind.ObjectMapper;
 import htsjdk.samtools.util.IOUtil;
+import org.jetbrains.annotations.Nullable;
 import org.junit.Assert;
 import org.junit.Test;
 import org.labkey.api.collections.IntHashMap;
@@ -46,6 +47,7 @@ public class SequenceJobSupportImpl implements SequenceAnalysisJobSupport, Seria
     private final Map<Long, AnalysisModel> _cachedAnalyses = new LongHashMap<>();
     private final Map<Integer, ReferenceGenome> _cachedGenomes = new IntHashMap<>();
     private final Map<String, Serializable> _cachedObjects = new HashMap<>();
+    private Integer _primaryGenomeForJob = null;
 
     private transient boolean _modifiedSinceSerialize = false;
 
@@ -194,6 +196,11 @@ public void cacheAnalysis(AnalysisModelImpl m, PipelineJob job, boolean allowRea
 
     @Override
     public void cacheGenome(ReferenceGenome m)
+    {
+        cacheGenome(m, false);
+    }
+
+    public void cacheGenome(ReferenceGenome m, boolean isPrimaryGenomeForJob)
     {
         markModified();
 
@@ -209,6 +216,10 @@ public void cacheGenome(ReferenceGenome m)
         }
 
         _cachedGenomes.put(key, m);
+        if (isPrimaryGenomeForJob)
+        {
+            _primaryGenomeForJob = key;
+        }
     }
 
     @Override
@@ -235,6 +246,11 @@ public Collection<ReferenceGenome> getCachedGenomes()
         return Collections.unmodifiableCollection(_cachedGenomes.values());
     }
 
+    public @Nullable Integer getPrimaryGenomeForJob()
+    {
+        return _primaryGenomeForJob;
+    }
+
     @Override
     public void cacheExpData(ExpData data)
     {
@@ -314,6 +330,7 @@ public void testSerializeWithMap() throws Exception
 
             js1._cachedReadsets.add(rs1);
             js1._cachedFilePaths.put(4L, new File("/"));
+            js1._primaryGenomeForJob = 1000;
 
             HashMap<Integer, Integer> map = new HashMap<>();
             map.put(1, 1);
@@ -339,6 +356,7 @@ public void testSerializeWithMap() throws Exception
             assertEquals("Readset list not serialized properly", 1, deserialized._cachedReadsets.size());
             assertEquals("Readset not deserialized with correct rowid", 100, deserialized._cachedReadsets.get(0).getRowId());
             assertEquals("Readset not deserialized with correct readsetid", 100, deserialized._cachedReadsets.get(0).getReadsetId().intValue());
+            assertEquals("PrimaryGenomeId not deserialized correctly", 1000, (int)deserialized._primaryGenomeForJob);
 
             assertNotNull("File map not serialized properly", deserialized._cachedFilePaths.get(4L));
             assertNotNull("Cached map not serialized properly", deserialized.getCachedObject("cachedMap",Map.class));

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/reference/CustomReferenceLibraryStep.java

@@ -10,6 +10,7 @@
 import org.labkey.api.sequenceanalysis.pipeline.PipelineStepProvider;
 import org.labkey.api.sequenceanalysis.pipeline.ReferenceLibraryStep;
 import org.labkey.api.sequenceanalysis.pipeline.ToolParameterDescriptor;
+import org.labkey.api.util.FileUtil;
 import org.labkey.api.writer.PrintWriters;
 import org.labkey.sequenceanalysis.pipeline.ReferenceGenomeImpl;
 
@@ -62,7 +63,7 @@ public CustomReferenceLibraryStep create(PipelineContext ctx)
 
     private File getExpectedFastaFile(File outputDirectory) throws PipelineJobException
     {
-        return new File(outputDirectory, "Custom.fasta");
+        return FileUtil.appendName(outputDirectory, "Custom.fasta");
     }
 
     @Override
@@ -79,7 +80,9 @@ public Output createReferenceFasta(File outputDirectory) throws PipelineJobExcep
         try (PrintWriter writer = PrintWriters.getPrintWriter(refFasta))
         {
             if (!refFasta.exists())
-                refFasta.createNewFile();
+            {
+                FileUtil.createNewFile(refFasta);
+            }
             writer.write(">" + name + "\n");
             seq = seq.replaceAll("\\s+", "");